class: inverse, center, middle
.pull-left[ ] .pull-right[ - GEO holds different types of biological datasets. - Very popular for submission of data accompanying publication. - Captures metadata, processed files and raw data. - GEO was not built for HTS data ]
.pull-left[ ] .pull-right[ - NCBI’s HTS specific repository. - Sequencing specific metadata. - Stores Raw data (in SRA format) - SRA format - requires SRA Toolkit]
.pull-left[ ] .pull-right[ - ENA acts as a european HTS repository. - Mirrors much of SRA. - Stores Raw data - No SRA formats - fastq by default.]
.pull-left[ ] .pull-right[ - Many repositories contain processed or unprocessed data. - These typically are the result or a consortium’s data release policies. - Good example is Encode site. - (https://www.encodeproject.org/) - UCSC has many useful links to genomics data in various formats. - (http://hgdownload.soe.ucsc.edu/downloads.html)]
Encode portal provides access to raw and processed/standardised results.
.pull-left[
] .pull-right[ - Other specialist repositories exist. - ReCount2 database provides standardised counts for user analysis. - Other databases like Immgen/Bodymap/expression atlas provide RNAseq for specific cells/tissues.]